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Target Prediction

miRanda (microRNA.org)

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. We present a computational method for whole-genome prediction of miRNA target genes. The method is validated using known examples.

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5
Average: 5 (2 votes)

TargetScan

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We predict regulatory targets of vertebrate microRNAs (miRNAs) by identifying mRNAs with conserved complementarity to the seed (nucleotides 2-7) of the miRNA. An overrepresentation of conserved adenosines flanking the seed complementary sites in mRNAs indicates that primary sequence determinants can supplement base pairing to specify miRNA target recognition.

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5
Average: 5 (2 votes)

miRNA - Target Gene Prediction at EMBL

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are short RNA molecules that regulate gene expression by binding to target messenger RNAs and by controlling protein production or causing RNA cleavage. To date, functions have been assigned to only a few of the hundreds of identified miRNAs, in part because of the difficulty in identifying their targets. The short length of miRNAs and the fact that their complementarity to target sequences is imperfect mean that target identification in animal genomes is not possible by standard sequence comparison methods.

Rating: 
5
Average: 5 (2 votes)

PicTar

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript. Different combinations of microRNAs are expressed in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs.

Rating: 
5
Average: 5 (2 votes)

RNAhybrid

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a few targets are known. In contrast to plant miRNAs, which usually bind nearly perfectly to their targets, animal miRNAs bind less tightly, with a few nucleotides being unbound, thus producing more complex secondary structures of miRNA/target duplexes. Here, we present a program, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs.

Rating: 
5
Average: 5 (2 votes)

DIANA-TarBase

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are approximately 22-nt RNA segments that are involved in the regulation of protein expression primarily by binding to one or more target sites on an mRNA transcript and inhibiting translation. MicroRNAs are likely to factor into multiple developmental pathways, multiple mechanisms of gene regulation, and underlie an array of inherited disease processes and phenotypic determinants. Several computational programs exist to predict miRNA targets in mammals, fruit flies, worms, and plants.

Rating: 
5
Average: 4.5 (2 votes)

DIANA-microT

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources.

Rating: 
4
Average: 3.5 (2 votes)

PITA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs are key regulators of gene expression, but the precise mechanisms underlying their interaction with their mRNA targets are still poorly understood. Here, we systematically investigate the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition. We experimentally show that mutations diminishing target accessibility substantially reduce microRNA-mediated translational repression, with effects comparable to those of mutations that disrupt sequence complementarity.

Rating: 
5
Average: 5 (2 votes)

miRecords

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are an important class of small noncoding RNAs capable of regulating other genes' expression. Much progress has been made in computational target prediction of miRNAs in recent years. More than 10 miRNA target prediction programs have been established, yet, the prediction of animal miRNA targets remains a challenging task. We have developed miRecords, an integrated resource for animal miRNA-target interactions.

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Average: 5 (1 vote)

miRDB

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are involved in many diverse biological processes and they may potentially regulate the functions of thousands of genes. However, one major issue in miRNA studies is the lack of bioinformatics programs to accurately predict miRNA targets. Animal miRNAs have limited sequence complementarity to their gene targets, which makes it challenging to build target prediction models with high specificity.

Rating: 
5
Average: 5 (2 votes)

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